Abstract
Abstract We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.
Highlights
A small fraction of the naturally occurring genetic diversity available in rice germplasm repositories around the world has been explored to date
Association mapping offers one way of identifying genes and quantitative trait loci (QTL) underlying quantitatively inherited variation in both plants and animals based on the analysis of diverse collections of wild and domesticated strains
Similar to traditional QTL mapping, genome-wide association mapping relies on the strength of linkage disequilibrium (LD) across a diverse population, and aims to identify relationships between markers and functional polymorphisms that determine traits of agronomic, aesthetic, and evolutionary interest
Summary
A small fraction of the naturally occurring genetic diversity available in rice germplasm repositories around the world has been explored to date. The rice research community supports a wide spectrum of both basic and applied activities aimed at understanding and utilizing natural variation These include evolutionary biology and population genetics inquiries, QTL mapping and gene discovery, allele mining and germplasm management, and pre-breeding and variety development, among others. Low-resolution assays are generally customdesigned for a particular population, and may be used to rapidly assay hundreds or thousands of individuals within a short time window Genotyping platforms such as the Illumina BeadXpress Reader provide rapid, low-cost 96 or 384-plex SNP genotyping for a variety of applications, including primary QTL analysis, NIL development and backcross conversion, varietal identification, quality control in the market or as part of germplasm management, to ensure outcrossing or inbreeding in a hybrid rice program, or to fine map a target region in a gene-discovery program. It can be used on a large number of individuals over many years if it is well designed and able to capture the essential components of variation in the breeders’ gene pool
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